Jan. 27th 2015

  • Goal : To identify baseline DNA methylation markers that predict the change in PHQ (Aim 1)

  • Model : PHQchange = a + b * BaselineMethylation + e

  • Sites : 437247

  • Sample size: 65

  • Multiple Testing Correction : Bonferroni

  • 5% MinP Cutoff - Raw PHQchange :

  • 5% MinP Cutoff - INV PHQchange :

Association Test

Raw PHQchange ~ Baseline Methylation

QQplot of pvals based on Raw PHQchange and CI

Results based on Raw PHQchange
CpG Chr Genes Pos beta pval p.adj size
cg25660390 17 NA 73073700 0.003 0.0e+00 0.0039 65
cg07219643 12 WSB2 118499016 0.001 1.0e-07 0.0327 65
cg15286044 10 CRTAC1 99789971 0.004 1.0e-07 0.0381 65
cg23932859 5 MEGF10 126625777 0.008 2.0e-07 0.0989 65
cg23679073 2 ZC3H15 187350909 0.002 3.0e-07 0.1408 65
cg26752884 11 JRKL;CCDC82 96123217 0.002 4.0e-07 0.1802 65
cg04992638 17 LOC100133991;C17orf46 43339328 0.002 4.0e-07 0.1889 65
cg25365565 6 HIST1H2BJ;HIST1H2AG 27101050 0.001 1.0e-06 0.4479 65
cg24190377 17 C17orf101 80350294 -0.001 1.1e-06 0.4659 65
cg22327690 17 TRIM37 57179774 -0.004 1.4e-06 0.6174 65

Studentized Residual QQ plots top 6 sites - raw PHQchange

[[1]]
63127 
   65 

[[2]]
63127 
   65 

[[3]]
63127 
   65 

[[4]]
50136 
   65 

[[5]]
63127 
   65 

[[6]]
63127 
   65

Leverage Plots top 6 sites - raw PHQchange

[[1]]
[1] 0

[[2]]
[1] 0

[[3]]
[1] 0

[[4]]
[1] 0

[[5]]
[1] 0

[[6]]
[1] 0

Cook's Distance - raw PHQchange

[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

[[4]]
NULL

[[5]]
NULL

[[6]]
NULL

PCA on top sites - Scree Plot

PCA on top sites - biplot

Association Test

INV PHQchange ~ Baseline Methylation

QQplot of pvals based on INV PHQchange and CI

QQplot: adj by covariates

QQplot: all sites 437247 vs thinned 106586

QQplot and CI: thinned sites 106586

QQplot and CI: thinned sites 106586

Results based on INV PHQchange
CpG Chr Genes Pos beta pval p.adj size
cg07219643 12 WSB2 118499016 0.004 1.0e-07 0.0510 65
cg23679073 2 ZC3H15 187350909 0.008 1.0e-07 0.0575 65
cg15286044 10 CRTAC1 99789971 0.013 7.0e-07 0.2946 65
cg00220389 17 NA 80455521 0.006 7.0e-07 0.3118 65
cg07696033 11 ALX4 44326410 0.008 1.1e-06 0.4659 65
cg20696752 17 LSM12 42143797 0.004 1.5e-06 0.6718 65
cg14613271 2 SLC5A7 108602931 0.013 2.2e-06 0.9507 65
cg02592615 6 HIVEP1 12012261 0.010 2.5e-06 1.0000 65
cg07399094 6 NA 3163461 0.007 2.9e-06 1.0000 65
cg26752884 11 JRKL;CCDC82 96123217 0.006 3.0e-06 1.0000 65

Results based on INV PHQchange for Candidate Genes
CpG Chr Genes Pos pval p.adj size
cg21702506 12 SLC6A15 85306648 0.0000668 0.0531 65
cg04506585 17 SOX9 70116204 0.0001620 0.1287 65
cg16521213 2 ACP1 277384 0.0001689 0.1341 65
cg11241206 11 BDNF 27723128 0.0008121 0.6448 65
cg07148459 18 DOK6 67462955 0.0014083 1.0000 65
cg27122725 5 NR3C1 142781723 0.0017026 1.0000 65
cg04123496 10 STK32C 134121596 0.0019147 1.0000 65
cg17160382 6 GJA1 121758980 0.0022011 1.0000 65
cg19088553 6 GRIK2 101901884 0.0023257 1.0000 65
cg24375465 6 GJA1 121767882 0.0025732 1.0000 65

Residual QQ plots top 6 sites - INV PHQchange

[[1]]
63127 
   65 

[[2]]
63127 
   65 

[[3]]
63127 
   65 

[[4]]
63127 
   65 

[[5]]
63127 
   65 

[[6]]
63127 
   65

Leverage Plots top 6 sites - INV PHQchange

[[1]]
[1] 0

[[2]]
[1] 0

[[3]]
[1] 0

[[4]]
[1] 0

[[5]]
[1] 0

[[6]]
[1] 0

Cook's Distance - INV PHQchange

[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

[[4]]
NULL

[[5]]
NULL

[[6]]
NULL

PCA on top sites - Scree Plot

PCA on top sites - biplot

Association Test

INV PHQchange ~ INV Baseline Methylation

QQplot pvals : INV PHQchange ~ INV Base Methylation

ScatterPlot: -log10 InvDiffMethyl vs -log10 DiffMethyl

Results based on INV PHQchange ~ INV Base Methylation
CpG Chr Genes Pos beta pval p.adj size
cg23679073 2 ZC3H15 187350909 0.602 1.0e-07 0.0496 65
cg07219643 12 WSB2 118499016 0.586 3.0e-07 0.1312 65
cg15286044 10 CRTAC1 99789971 0.571 7.0e-07 0.3004 65
cg26880187 12 ERBB3 56473976 0.568 8.0e-07 0.3505 65
cg00220389 17 NA 80455521 0.568 8.0e-07 0.3573 65
cg02592615 6 HIVEP1 12012261 0.565 1.0e-06 0.4264 65
cg25429640 5 UNC5A 176302913 0.560 1.3e-06 0.5539 65
cg02370807 5 HNRNPAB 177632259 0.560 1.3e-06 0.5593 65
cg07696033 11 ALX4 44326410 0.557 1.5e-06 0.6386 65
cg26752884 11 JRKL;CCDC82 96123217 0.554 1.7e-06 0.7632 65

Residual QQ plots top 6 sites

[[1]]
63127 
   65 

[[2]]
54075 
    1 

[[3]]
50136 
   65 

[[4]]
50136 
   65 

[[5]]
63127 
   65 

[[6]]
63127 
   65

Leverage Plots top 6 sites

[[1]]
[1] 0

[[2]]
[1] 0

[[3]]
[1] 0

[[4]]
[1] 0

[[5]]
[1] 0

[[6]]
[1] 0

Cook's Distance : INV PHQchange ~ INV Base Methylation

[[1]]
NULL

[[2]]
NULL

[[3]]
NULL

[[4]]
NULL

[[5]]
NULL

[[6]]
NULL

PCA on top sites - Scree Plot

PCA on top sites - biplot